Revision 31498
Added by Marek Horst about 10 years ago
| modules/icm-iis-mainworkflows/trunk/src/main/resources/eu/dnetlib/iis/mainworkflows/common/import/job.properties | ||
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| 17 | 17 |
#przetestowac czy plaintexty wos sa prawidlowo wyciagane zarowno w trybie sprawdzania instenia jak i bez tego trybu |
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#approved_objectstores_csv=a1a35f9d-dc12-44e0-8781-d8273f5ef017_T2JqZWN0U3RvcmVEU1Jlc291cmNlcy9PYmplY3RTdG9yZURTUmVzb3VyY2VUeXBl |
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metadataextraction_default_cache_location=/cache/metadataextraction_2014-09-26
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metadataextraction_default_cache_location=/cache/metadataextraction |
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mimetypes_pdf=pdf,application/pdf |
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mimetypes_text=text |
| modules/icm-iis-mainworkflows/trunk/src/main/resources/eu/dnetlib/iis/mainworkflows/common/import/oozie_app/import.txt | ||
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| 10 | 10 |
metadataextraction_cached classpath eu/dnetlib/iis/mainworkflows/metadataextraction/cached_by_checksum/oozie_app |
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transformers_common_union3 classpath eu/dnetlib/iis/transformers/common/union3/oozie_app |
| 12 | 12 |
transformers_idextractor classpath eu/dnetlib/iis/transformers/importer/documentmetadata/idextractor/oozie_app |
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transformers_externalidtooaid classpath eu/dnetlib/iis/transformers/importer/documentmetadata/externalidtooaid/oozie_app |
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transformers_externalidtooaid classpath eu/dnetlib/iis/transformers/importer/documentmetadata/externalidtooaid/oozie_app |
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ingest_pmc_idmapping_pmidtooaid classpath eu/dnetlib/iis/ingest/pmc/idmapping/pmidtooaid/oozie_app |
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| modules/icm-iis-mainworkflows/trunk/src/main/resources/eu/dnetlib/iis/mainworkflows/common/import/oozie_app/workflow.xml | ||
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| 691 | 691 |
</property> |
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</configuration> |
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</sub-workflow> |
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<ok to="generate_pmid_to_oaid_mocked_input"/>
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<ok to="ingest_pmc_idmapping_pmidtooaid"/>
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<error to="fail"/> |
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</action> |
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<action name="generate_pmid_to_oaid_mocked_input"> |
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<java> |
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<!-- The data generated by this node is deleted in this section --> |
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<prepare> |
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<delete path="${nameNode}${workingDir}/pmid_to_oaid_producer" />
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<mkdir path="${nameNode}${workingDir}/pmid_to_oaid_producer" />
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</prepare> |
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<action name="ingest_pmc_idmapping_pmidtooaid"> |
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<sub-workflow> |
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<app-path>${wf:appPath()}/ingest_pmc_idmapping_pmidtooaid</app-path>
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<propagate-configuration/> |
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<configuration> |
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<property> |
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<name>mapred.job.queue.name</name>
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<value>${queueName}</value>
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<name>workingDir</name>
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<value>${workingDir}/ingest_pmc_idmapping_pmidtooaid/working_dir</value>
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| 711 | 706 |
</property> |
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<property> |
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<name>input_document_nlm</name> |
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<value>${workingDir}/import_plaintext_pmc/imported</value>
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</property> |
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<property> |
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<name>output</name> |
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<value>${workingDir}/ingest_pmc_idmapping_pmidtooaid/out</value>
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</property> |
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</configuration> |
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<!-- This is simple wrapper for the Java code --> |
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<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class> |
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<!-- The business Java code that gets to be executed --> |
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<arg>eu.dnetlib.iis.core.java.jsonworkflownodes.Producer</arg> |
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<!-- Specification of the output ports --> |
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<arg>-C{pmid_to_oaid,
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eu.dnetlib.iis.common.schemas.IdentifierMapping, |
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eu/dnetlib/iis/mainworkflows/data/empty.json}</arg> |
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<arg>-SworkingDir=${workingDir}/pmid_to_oaid_producer/working_dir</arg>
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<arg>-Opmid_to_oaid=${workingDir}/pmid_to_oaid_producer/pmid_to_oaid</arg>
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</java> |
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</sub-workflow> |
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<ok to="ingest_pmc_citations"/> |
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<error to="fail"/> |
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</action> |
| ... | ... | |
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</property> |
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<property> |
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<name>input_pmid_to_oaid</name> |
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<value>${workingDir}/pmid_to_oaid_producer/pmid_to_oaid</value>
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<value>${workingDir}/ingest_pmc_idmapping_pmidtooaid/out</value>
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</property> |
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<property> |
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<name>output_citation</name> |
Also available in: Unified diff
#757 hooking up ingest_pmc_idmapping_pmidtooaid subworkflow with mainworkflows/common/import. From now on citations are matched by pmid as well.